List of works - Kresten Lindorff-Larsen

A Monte Carlo Study of the Early Steps of Functional Amyloid Formation

scientific article published on 8 January 2016

A Robust Proton Flux (pHlux) Assay for Studying the Function and Inhibition of the Influenza A M2 Proton Channel

scientific article published on 03 October 2018

A Soluble, Folded Protein without Charged Amino Acid Residues

scientific article

A Sticky Cage can Slow Down Folding ⬇️

scientific article published on March 5, 2013

A Two-step Protein Quality Control Pathway for a Misfolded DJ-1 Variant in Fission Yeast ⬇️

scientific article

A combined computational and structural model of the full-length human prolactin receptor

scientific article

A dual-reporter system for investigating and optimizing protein translation and folding in E. coli

scientific article published on 19 October 2021

A phosphorylation-motif for tuneable helix stabilisation in intrinsically disordered proteins - Lessons from the sodium proton exchanger 1 (NHE1).

scientific article published on 26 May 2017

A structural biology community assessment of AlphaFold 2 applications

A structural biology community assessment of AlphaFold2 applications

scientific article published in 2022

Accurate model of liquid–liquid phase behavior of intrinsically disordered proteins from optimization of single-chain properties

scientific article published in 2021

An Efficient Method for Estimating the Hydrodynamic Radius of Disordered Protein Conformations

scientific article published in August 2017

Atomic-Level Characterization of the Structural Dynamics of Proteins ⬇️

scientific article (publication date: 15 October 2010)

Atomic-level description of ubiquitin folding

scientific article published on 15 March 2013

Atomistic description of the folding of a dimeric protein

scientific article published on 15 August 2013

Automated Event Detection and Activity Monitoring in Long Molecular Dynamics Simulations

article

BPPred: a Web-based computational tool for predicting biophysical parameters of proteins

scientific article

Barley lipid transfer protein, LTP1, contains a new type of lipid-like post-translational modification.

scientific article published on 2 July 2001

Barnaba: software for analysis of nucleic acid structures and trajectories

scientific article published on 12 November 2018

Bioinformatics analysis identifies several intrinsically disordered human E3 ubiquitin-protein ligases

scientific article published on 25 February 2016

Biomolecular conformational changes and ligand binding: from kinetics to thermodynamics

scientific article published on 12 July 2017

Biophysical experiments and biomolecular simulations: A perfect match?

scientific article published on 01 July 2018

Blocking protein quality control to counter hereditary cancers

scientific article published on 4 August 2017

Calculation of mutational free energy changes in transition states for protein folding

scientific article

Characterization of the residual structure in the unfolded state of the Δ131Δ fragment of staphylococcal nuclease

article

Co-Chaperones in Targeting and Delivery of Misfolded Proteins to the 26S Proteasome

scientific article published on 04 August 2020

Co-evolution of drug resistance and broadened substrate recognition in HIV protease variants isolated from an <i>Escherichia coli</i> genetic selection system

scientific article published in 2022

Combining experiments and simulations using the maximum entropy principle

scientific article

Combining molecular dynamics simulations with small-angle X-ray and neutron scattering data to study multi-domain proteins in solution

scientific article published on 27 April 2020

Communication routes in ARID domains between distal residues in helix 5 and the DNA-binding loops

scientific article

Comparing molecular dynamics force fields in the essential subspace.

scientific article

Comparison of the transition state ensembles for folding of Im7 and Im9 determined using all-atom molecular dynamics simulations with phi value restraints

scientific article (publication date: 15 February 2004)

Computational Redesign of Thioredoxin Is Hypersensitive toward Minor Conformational Changes in the Backbone Template

scientific article

Computational and cellular studies reveal structural destabilization and degradation of MLH1 variants in Lynch syndrome

scientific article published on 07 November 2019

Computational design and experimental testing of the fastest-folding β-sheet protein

scientific article

Conformational Changes and Free Energies in a Proline Isomerase

Conformational Rigidity and Protein Dynamics at Distinct Timescales Regulate PTP1B Activity and Allostery.

scientific article published on February 2017

Conformational ensembles of RNA oligonucleotides from integrating NMR and molecular simulations.

scientific article

Conformational fluctuations affect protein alignment in dilute liquid crystal media

scientific article

Cryo-EM reveals the architecture of placental malaria VAR2CSA and provides molecular insight into chondroitin sulfate binding

scientific article published on 19 May 2021

DNA-binding protects p53 from interactions with cofactors involved in transcription-independent functions

scientific article

Detection of initiation sites in protein folding of the four helix bundle ACBP by chemical shift analysis

article

Determination of an ensemble of structures representing the denatured state of the bovine acyl-coenzyme a binding protein

scientific article published in March 2004

Diversity-Oriented Peptide Stapling: A Third Generation Copper-Catalysed Azide-Alkyne Cycloaddition Stapling and Functionalisation Strategy

scientific article published on 20 January 2017

ENCORE: Software for Quantitative Ensemble Comparison.

scientific article published on 27 October 2015

Enhancing coevolution-based contact prediction by imposing structural self-consistency of the contacts

scientific article published on 24 July 2018

Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks

scientific article published on 29 November 2021

Evaluating the effects of cutoffs and treatment of long-range electrostatics in protein folding simulations

scientific article published in 2012

Experimental parameterization of an energy function for the simulation of unfolded proteins

scientific article published on 7 September 2007

Exploiting hydrophobicity for efficient production of transmembrane helices for structure determination by NMR spectroscopy

scientific article published on 26 August 2015

Fitting Corrections to an RNA Force Field Using Experimental Data

scientific article published on 23 May 2019

Fitting Side-Chain NMR Relaxation Data Using Molecular Simulations

scientific article published on 22 July 2021

Folliculin variants linked to Birt-Hogg-Dubé syndrome are targeted for proteasomal degradation

scientific article published on 02 November 2020

Force Field Effects in Simulations of Flexible Peptides with Varying Polyproline II Propensity

scientific article published on 15 September 2021

Formation of native and non-native interactions in ensembles of denatured ACBP molecules from paramagnetic relaxation enhancement studies

scientific article published on 27 January 2005

Frequency adaptive metadynamics for the calculation of rare-event kinetics

scientific article published on 01 August 2018

How fast-folding proteins fold

scientific article

How robust are protein folding simulations with respect to force field parameterization?

scientific article published on May 2011

Improved side-chain torsion potentials for the Amber ff99SB protein force field

scientific article

Improving Martini 3 for Disordered and Multidomain Proteins

scientific article published on 04 April 2022

Interaction Networks in Protein Folding via Atomic-Resolution Experiments and Long-Time-Scale Molecular Dynamics Simulations

scientific article

Interpreting Dynamically-Averaged Scalar Couplings in Proteins

article

Long-timescale molecular dynamics simulations of protein structure and function.

scientific article

Mapping Long-Range Interactions in α-Synuclein using Spin-Label NMR and Ensemble Molecular Dynamics Simulations

article

Mapping the Universe of RNA Tetraloop Folds.

scientific article published on 30 June 2017

Mapping the degradation pathway of a disease-linked aspartoacylase variant

scientific article published on 29 April 2021

Mapping transiently formed and sparsely populated conformations on a complex energy landscape

scientific article published on 23 August 2016

Mg 2+ -dependent conformational equilibria in CorA: an integrated view on transport regulation

Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins

scientific article

Millisecond-scale molecular dynamics simulations on Anton

article published in 2009

Monte Carlo Sampling of Protein Folding by Combining an All-Atom Physics-Based Model with a Native State Bias

scientific article published on 06 September 2018

PHAISTOS: a framework for Markov chain Monte Carlo simulation and inference of protein structure

scientific article

Parallel protein-unfolding pathways revealed and mapped

Paths of long-range communication in the E2 enzymes of family 3: a molecular dynamics investigation

scientific article

Picosecond to Millisecond Structural Dynamics in Human Ubiquitin

scientific article published on 15 April 2016

Predicting the impact of Lynch syndrome-causing missense mutations from structural calculations

scientific article

Principles of conduction and hydrophobic gating in K+ channels

scientific article

Probabilistic Determination of Native State Ensembles of Proteins

scientific article published on 30 June 2014

Protein folding and the organization of the protein topology universe.

scientific article

Protein folding kinetics and thermodynamics from atomistic simulation

scientific article

Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics

scientific article (publication date: 2013)

Random Mutagenesis Analysis of the Influenza A M2 Proton Channel Reveals Novel Resistance Mutants

scientific article published on 03 October 2018

Relation between native ensembles and experimental structures of proteins

scholarly article

Robust Estimation of Diffusion-Optimized Ensembles for Enhanced Sampling

scientific article published on 28 January 2014

Role of protein dynamics in transmembrane receptor signalling

scientific article published on 11 November 2017

Side chain to main chain hydrogen bonds stabilize a polyglutamine helix in a transcription factor

scientific article published on 02 May 2019

Similarity measures for protein ensembles

scientific article published on 15 January 2009

Simultaneous determination of protein structure and dynamics.

scientific article

Structural and functional variation of chitin-binding domains of a lytic polysaccharide monooxygenase from Cellvibrio japonicus

scientific article published on 17 August 2021

Structural basis of client specificity in mitochondrial membrane-protein chaperones

scientific article published on 18 December 2020

Structure and dynamics of a nanodisc by integrating NMR, SAXS and SANS experiments with molecular dynamics simulations

scientific article published on 30 July 2020

Structure and dynamics of an unfolded protein examined by molecular dynamics simulation

scientific article published on 16 February 2012

Structure of a Functional Amyloid Protein Subunit Computed Using Sequence Variation

article

Structure of the Bacterial Cytoskeleton Protein Bactofilin by NMR Chemical Shifts and Sequence Variation

scientific article

Structure of the regulatory apparatus of a calcium-dependent protein kinase (CDPK): a novel mode of calmodulin-target recognition

scientific article published on 20 December 2005

Substrate-induced conformational dynamics of the dopamine transporter.

scientific article published on 20 June 2019

Systematic validation of protein force fields against experimental data

scientific article (publication date: 2012)

The Role of Protein Loops and Linkers in Conformational Dynamics and Allostery

scientific article published on 18 February 2016

Thiol Alkylation below Neutral pH

article by Kresten Lindorff-Larsen & Jakob R. Winther published November 2000 in Analytical Biochemistry

Topological constraints and modular structure in the folding and functional motions of GlpG, an intramembrane protease

scientific article published on 8 February 2016

Toward mechanistic models for genotype-phenotype correlations in phenylketonuria using protein stability calculations

scientific article published on 25 January 2019

Transition state contact orders correlate with protein folding rates

scientific article published in September 2005

Transition states for protein folding have native topologies despite high structural variability

scientific article

Understanding single-pass transmembrane receptor signaling from a structural viewpoint-what are we missing?

scientific article

Variational Optimization of an All-Atom Implicit Solvent Force Field to Match Explicit Solvent Simulation Data

scientific article

What Will Computational Modeling Approaches Have to Say in the Era of Atomistic Cryo-EM Data?

scientific article published on 24 February 2020

List of works by Kresten Lindorff-Larsen

A Monte Carlo Study of the Early Steps of Functional Amyloid Formation

A Robust Proton Flux (pHlux) Assay for Studying the Function and Inhibition of the Influenza A M2 Proton Channel

A Soluble, Folded Protein without Charged Amino Acid Residues

A Sticky Cage can Slow Down Folding ⬇️

A Two-step Protein Quality Control Pathway for a Misfolded DJ-1 Variant in Fission Yeast ⬇️

A combined computational and structural model of the full-length human prolactin receptor

A dual-reporter system for investigating and optimizing protein translation and folding in E. coli

A phosphorylation-motif for tuneable helix stabilisation in intrinsically disordered proteins - Lessons from the sodium proton exchanger 1 (NHE1).

A structural biology community assessment of AlphaFold 2 applications

A structural biology community assessment of AlphaFold2 applications

Accurate model of liquid–liquid phase behavior of intrinsically disordered proteins from optimization of single-chain properties

An Efficient Method for Estimating the Hydrodynamic Radius of Disordered Protein Conformations

Atomic-Level Characterization of the Structural Dynamics of Proteins ⬇️

Atomic-level description of ubiquitin folding

Atomistic description of the folding of a dimeric protein

Automated Event Detection and Activity Monitoring in Long Molecular Dynamics Simulations

BPPred: a Web-based computational tool for predicting biophysical parameters of proteins

Barley lipid transfer protein, LTP1, contains a new type of lipid-like post-translational modification.

Barnaba: software for analysis of nucleic acid structures and trajectories

Bioinformatics analysis identifies several intrinsically disordered human E3 ubiquitin-protein ligases

Biomolecular conformational changes and ligand binding: from kinetics to thermodynamics

Biophysical experiments and biomolecular simulations: A perfect match?

Blocking protein quality control to counter hereditary cancers

Calculation of mutational free energy changes in transition states for protein folding

Characterization of the residual structure in the unfolded state of the Δ131Δ fragment of staphylococcal nuclease

Co-Chaperones in Targeting and Delivery of Misfolded Proteins to the 26S Proteasome

Co-evolution of drug resistance and broadened substrate recognition in HIV protease variants isolated from an <i>Escherichia coli</i> genetic selection system

Combining experiments and simulations using the maximum entropy principle

Combining molecular dynamics simulations with small-angle X-ray and neutron scattering data to study multi-domain proteins in solution

Communication routes in ARID domains between distal residues in helix 5 and the DNA-binding loops

Comparing molecular dynamics force fields in the essential subspace.

Comparison of the transition state ensembles for folding of Im7 and Im9 determined using all-atom molecular dynamics simulations with phi value restraints

Computational Redesign of Thioredoxin Is Hypersensitive toward Minor Conformational Changes in the Backbone Template

Computational and cellular studies reveal structural destabilization and degradation of MLH1 variants in Lynch syndrome

Computational design and experimental testing of the fastest-folding β-sheet protein

Conformational Changes and Free Energies in a Proline Isomerase

Conformational Rigidity and Protein Dynamics at Distinct Timescales Regulate PTP1B Activity and Allostery.

Conformational ensembles of RNA oligonucleotides from integrating NMR and molecular simulations.

Conformational fluctuations affect protein alignment in dilute liquid crystal media

Cryo-EM reveals the architecture of placental malaria VAR2CSA and provides molecular insight into chondroitin sulfate binding

DNA-binding protects p53 from interactions with cofactors involved in transcription-independent functions

Detection of initiation sites in protein folding of the four helix bundle ACBP by chemical shift analysis

Determination of an ensemble of structures representing the denatured state of the bovine acyl-coenzyme a binding protein

Diversity-Oriented Peptide Stapling: A Third Generation Copper-Catalysed Azide-Alkyne Cycloaddition Stapling and Functionalisation Strategy

ENCORE: Software for Quantitative Ensemble Comparison.

Enhancing coevolution-based contact prediction by imposing structural self-consistency of the contacts

Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks

Evaluating the effects of cutoffs and treatment of long-range electrostatics in protein folding simulations

Experimental parameterization of an energy function for the simulation of unfolded proteins

Exploiting hydrophobicity for efficient production of transmembrane helices for structure determination by NMR spectroscopy

Fitting Corrections to an RNA Force Field Using Experimental Data

Fitting Side-Chain NMR Relaxation Data Using Molecular Simulations

Folliculin variants linked to Birt-Hogg-Dubé syndrome are targeted for proteasomal degradation

Force Field Effects in Simulations of Flexible Peptides with Varying Polyproline II Propensity

Formation of native and non-native interactions in ensembles of denatured ACBP molecules from paramagnetic relaxation enhancement studies

Frequency adaptive metadynamics for the calculation of rare-event kinetics

How fast-folding proteins fold

How robust are protein folding simulations with respect to force field parameterization?

Improved side-chain torsion potentials for the Amber ff99SB protein force field

Improving Martini 3 for Disordered and Multidomain Proteins

Interaction Networks in Protein Folding via Atomic-Resolution Experiments and Long-Time-Scale Molecular Dynamics Simulations

Interpreting Dynamically-Averaged Scalar Couplings in Proteins

Long-timescale molecular dynamics simulations of protein structure and function.

Mapping Long-Range Interactions in α-Synuclein using Spin-Label NMR and Ensemble Molecular Dynamics Simulations

Mapping the Universe of RNA Tetraloop Folds.

Mapping the degradation pathway of a disease-linked aspartoacylase variant

Mapping transiently formed and sparsely populated conformations on a complex energy landscape

Mg 2+ -dependent conformational equilibria in CorA: an integrated view on transport regulation

Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins

Millisecond-scale molecular dynamics simulations on Anton

Monte Carlo Sampling of Protein Folding by Combining an All-Atom Physics-Based Model with a Native State Bias

PHAISTOS: a framework for Markov chain Monte Carlo simulation and inference of protein structure

Parallel protein-unfolding pathways revealed and mapped

Paths of long-range communication in the E2 enzymes of family 3: a molecular dynamics investigation

Picosecond to Millisecond Structural Dynamics in Human Ubiquitin

Predicting the impact of Lynch syndrome-causing missense mutations from structural calculations

Principles of conduction and hydrophobic gating in K+ channels

Probabilistic Determination of Native State Ensembles of Proteins

Protein folding and the organization of the protein topology universe.